From 21695cd279a67bea8c4467c7108dfce03be799d0 Mon Sep 17 00:00:00 2001
From: vcfrmgit <frm@uchc.edu>
Date: Thu, 5 Aug 2021 01:22:04 -0400
Subject: [PATCH] Add vcell-web module (bug fix)

---
 vcell-web/pom.xml                             | 27 ++++++++++---------
 .../main/java/org/vcell/web/MainService.java  | 16 ++++-------
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/vcell-web/pom.xml b/vcell-web/pom.xml
index c2677579a4..318b6c8ada 100644
--- a/vcell-web/pom.xml
+++ b/vcell-web/pom.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<!-- <project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> -->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.vcell</groupId>
@@ -10,8 +12,14 @@
 
   <artifactId>vcell-web</artifactId>
   
-  	<name>Virtual Cell Project</name>
-	<description>The Virtual Cell client and server</description>
+  <!--   <name>vcell-web</name>
+  <url>http://maven.apache.org</url>
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+ -->  
+  	<name>vcell-web</name>
+	<description>VCell Data Export Web Interface</description>
 	<url>http://vcell.org/</url>
 	<inceptionYear>1997</inceptionYear>
 	<organization>
@@ -79,12 +87,7 @@
 	</properties>
 	
   
-<!--   <name>vcell-web</name>
-  <url>http://maven.apache.org</url>
-  <properties>
-    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-  </properties>
- -->  
+
   
 <!-- * description: element is missing
 * inceptionYear: element is missing
@@ -119,10 +122,10 @@
     </dependency>
     
     <!-- https://mvnrepository.com/artifact/org.hdfgroup/hdf-java -->
-<dependency>
+<!-- <dependency>
     <groupId>org.hdfgroup</groupId>
     <artifactId>hdf-java</artifactId>
     <version>2.6.1</version>
 </dependency>
-  </dependencies>
+ -->  </dependencies>
 </project>
diff --git a/vcell-web/src/main/java/org/vcell/web/MainService.java b/vcell-web/src/main/java/org/vcell/web/MainService.java
index cab338a545..d4250b6ff2 100644
--- a/vcell-web/src/main/java/org/vcell/web/MainService.java
+++ b/vcell-web/src/main/java/org/vcell/web/MainService.java
@@ -9,13 +9,9 @@
 import java.net.URLDecoder;
 import java.nio.charset.Charset;
 import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.security.KeyStore;
 import java.security.SecureRandom;
-import java.sql.Connection;
 import java.sql.SQLException;
-import java.sql.Statement;
 import java.text.DateFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -42,7 +38,6 @@
 import org.apache.http.HttpStatus;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.utils.URLEncodedUtils;
-import org.apache.http.entity.ByteArrayEntity;
 import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.bootstrap.HttpServer;
@@ -52,7 +47,6 @@
 import org.apache.http.ssl.SSLContexts;
 import org.vcell.db.ConnectionFactory;
 import org.vcell.db.DatabaseService;
-import org.vcell.db.DatabaseSyntax;
 import org.vcell.db.KeyFactory;
 import org.vcell.util.ConfigurationException;
 import org.vcell.util.DataAccessException;
@@ -71,8 +65,6 @@
 import cbit.vcell.message.messages.MessageConstants;
 import cbit.vcell.modeldb.AdminDBTopLevel;
 import cbit.vcell.modeldb.DatabaseServerImpl;
-import cbit.vcell.modeldb.DbDriver;
-import cbit.vcell.modeldb.LocalAdminDbServer;
 import cbit.vcell.resource.PropertyLoader;
 import cbit.vcell.resource.ResourceUtil;
 import cbit.vcell.simdata.Cachetable;
@@ -351,15 +343,17 @@ public int compare(BioModelInfo o1, BioModelInfo o2) {
 					if(bioModelContextName != null) {
 						//dataspaceName.replace("/", "fwdslsh");
 		    			int bmContextID = Hdf5Utils.createGroup(bioModelGroupID, bioModelContextName.replace("/", "fwdslsh"));
-//    			        				ArrayList<IJSimInfo> ijSimInfos = new ArrayList<>();
+		    			Hdf5Utils.insertAttribute(bmContextID, "type", bioModelInfo.getBioModelChildSummary().getAppTypes()[i].toString());
+		    			Hdf5Utils.insertAttribute(bmContextID, "dim", bioModelInfo.getBioModelChildSummary().getGeometryDimensions()[i]+"");
+		    			Hdf5Utils.insertAttribute(bmContextID, "geoName", bioModelInfo.getBioModelChildSummary().getGeometryNames()[i]);
 		    			if(bioModelInfo.getBioModelChildSummary().getSimulationNames(bioModelContextName) != null &&
 		    					bioModelInfo.getBioModelChildSummary().getSimulationNames(bioModelContextName).length > 0) {
 		    				ArrayList<String> simNameArr = new ArrayList<String>();
 		    				for(String simName:bioModelInfo.getBioModelChildSummary().getSimulationNames(bioModelContextName)) {
 		    					simNameArr.add(simName);
-//    				        					simNameArr.add((bioModelInfo.getSimID(simName)==null?"null":bioModelInfo.getSimID(simName).toString()));
+//    				        	simNameArr.add((bioModelInfo.getSimID(simName)==null?"null":bioModelInfo.getSimID(simName).toString()));
 		    				}
-							Hdf5Utils.insertStrings(bmContextID, "sims", new long[] {2,bioModelInfo.getBioModelChildSummary().getSimulationNames(bioModelContextName).length},simNameArr);
+							Hdf5Utils.insertStrings(bmContextID, "sims", new long[] {bioModelInfo.getBioModelChildSummary().getSimulationNames(bioModelContextName).length,1},simNameArr);
 		    			}
 		    			H5.H5Gclose(bmContextID);
 //    			    					IJContextInfo ijContextInfo = new IJContextInfo(bioModelContextName,bioModelInfo.getBioModelChildSummary().getAppTypes()[i],bioModelInfo.getBioModelChildSummary().getGeometryDimensions()[i],bioModelInfo.getBioModelChildSummary().getGeometryNames()[i],ijSimInfos);